Unpacking them should not have any effect on your game whatsoever. Doing so does not delete the file you unpacked, rather it copies the files that were inside the .pak and places them in a new folder using its root directory as the base of where it unpacks (ie if you unpack patch_1.pak in the data\packs folder, XPAK will place all the files in the appropriate subfolders under data\packs\data). Even if you were to unpack the files into the proper folders it still wouldn't make any difference, since the game doesn't really care about files within normal folders when there's a file of the same name in one of the .pak files.
In short: it shouldn't make any difference at all

But if you want to be on the safe side, you can always copy the .pak to a temporary folder, though this shouldn't be necessary.
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